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Marle only falls out of favor after you've reached New Game+.
What happens is that once you get everyone's ultimate gear, the game kind of breaks down mechanically. Auto attacks are free, tend to hit as hard or even harder than techniques, and even if they don't, they will do more damage than a Double or even Triple technique. And Marle's best weapons are kind of weak compared to everyone else's.
Don't need a dedicated healer, because you pummel your way through everything and the defensive bonuses from gear get kind of crazy. And even if you do need healing, megaelixirs start falling into your lap once you figure out that Ayla's charm skill is a game-breaker in of itself.
Marle is one of the best characters, being a participant in some of the best combos in the game, but once you reach a certain power ceiling, she lags behind because her skills aren't really needed.